Computational protocol: Age dependent forebrain structural changes in mice deficient in the autism associated gene Met tyrosine kinase☆

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Protocol publication

[…] Post-imaging analysis for volume and area was performed using NIH ImageJ software (version 1.43u). shows the boundaries of the regions of interest that were measured in the coronal plane (A–C), as well as in the mid-sagittal plane (D). Measurements of the whole brain included all structures from the rostral extent of the cerebral cortex (bregma ~ 4.0 mm, ()) to the caudal brainstem-spinal cord juncture (bregma ~ 8.5 mm). The area of the cerebral cortex was measured from pia to white matter, with boundaries defined rostrally by the emergence of the olfactory bulb, caudally by the plane in which the deep white matter (dorsal hippocampal commissure) was no longer visible, and ventrally by the rhinal sulcus, end of the CC, or level of the anterior commissure (from caudal to rostral). Measurements of the hippocampus include both the upper and lower leaves. The hippocampus is bordered dorsally and laterally by the corpus callosum (CC), lateral ventricles, or fimbria, and ventrally and medially by the thalamus, third ventricle, alveus hippocampus, brachium superior colliculus, or optic tract.Measurements of the striatum include the caudate and putamen. The boundaries of the striatum were defined medially by the lateral ventricles and internal capsule, laterally and dorsally by the external capsule, and ventrally by the anterior commissure. Measurements of the thalamus include both thalamic and hypothalamic nuclei. The boundaries of this region were defined laterally by the internal capsule and cerebral peduncle, dorsally by the hippocampus, and ventrally by the ventral surface of the brain. Measurements of the thalamus did not include the third ventricle or posterior commissure. [...] Four brains were imaged for each of the P30 control, P30 Met–Emx1, adult control, and Met–Emx1 groups. The images analyzed represent 100 μm thick sections, with a voxel size of 0.1 × 0.1 × 0.1 mm. With the exception of measurements of the whole brain, area measurements were taken separately for each hemisphere. The distributions of cross-sectional areas across different rostrocaudal levels were compared between control and Met–Emx1 mice at each age with Kolmogorov–Smirnov (K–S). For volume comparisons, measurements were made for the left and right hemispheres for each structure. The overall volume of each structure was compared using a three-way ANOVA in SigmaPlot12 (Systat Software, San Jose, CA) followed by a Bonferroni t-test as appropriate. Cortical thickness and surface area were compared between adult control and Met–Emx1 mice using a Student's t test. […]

Pipeline specifications

Software tools ImageJ, SigmaPlot
Applications Miscellaneous, Microscopic phenotype analysis
Organisms Mus musculus, Homo sapiens